| ! | Bio.Utils.BitVector |
| & | Bio.RealWorld.ENCODE |
| addTerm | Bio.GO |
| AlignFn | Bio.Motif.Alignment |
| alignment | Bio.Motif.Alignment |
| alignmentBy | Bio.Motif.Alignment |
| alphabet | Bio.Seq |
| as | Bio.RealWorld.ENCODE |
| asBed | Bio.Data.Bed.Types, Bio.Data.Bed |
| assayIs | Bio.RealWorld.ENCODE |
| BAM | Bio.Data.Bam |
| bamToBed | Bio.Data.Bam |
| bamToBedC | Bio.Data.Bam |
| bamToFastq | Bio.Data.Bam |
| bamToFastqC | Bio.Data.Bam |
| BaseMap | |
| 1 (Type/Class) | Bio.Data.Bed.Utils |
| 2 (Data Constructor) | Bio.Data.Bed.Utils |
| baseMap | Bio.Data.Bed.Utils |
| Basic | Bio.Seq |
| BED | |
| 1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
| 2 (Data Constructor) | Bio.Data.Bed.Types |
| BED3 | |
| 1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
| 2 (Data Constructor) | Bio.Data.Bed.Types |
| BEDConvert | Bio.Data.Bed.Types, Bio.Data.Bed |
| BEDExt | |
| 1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
| 2 (Data Constructor) | Bio.Data.Bed.Types, Bio.Data.Bed |
| BEDLike | Bio.Data.Bed.Types, Bio.Data.Bed |
| bedToTree | Bio.Data.Bed |
| BEDTree | Bio.Data.Bed.Types, Bio.Data.Bed |
| BG | Bio.Motif |
| binarySearch | Bio.Utils.Functions |
| binarySearchBy | Bio.Utils.Functions |
| binarySearchByBounds | Bio.Utils.Functions |
| binBySize | Bio.Utils.Misc |
| binBySizeLeft | Bio.Utils.Misc |
| binBySizeOverlap | Bio.Utils.Misc |
| bins | Bio.Utils.Misc |
| BioID | Bio.RealWorld.ID |
| BioSeq | Bio.Seq |
| BioSeq' | Bio.Seq |
| BitMVector | Bio.Utils.BitVector |
| BitVector | |
| 1 (Type/Class) | Bio.Utils.BitVector |
| 2 (Data Constructor) | Bio.Utils.BitVector |
| Bkgd | Bio.Motif |
| bpPvalue | Bio.Data.Bed.Types |
| bpQvalue | Bio.Data.Bed.Types |
| bpSignal | Bio.Data.Bed.Types |
| BroadPeak | |
| 1 (Type/Class) | Bio.Data.Bed.Types |
| 2 (Data Constructor) | Bio.Data.Bed.Types |
| buildTree | Bio.Motif.Merge |
| CDF | |
| 1 (Type/Class) | Bio.Motif |
| 2 (Data Constructor) | Bio.Motif |
| cdf | Bio.Motif |
| cdf' | Bio.Motif |
| cellIs | Bio.RealWorld.ENCODE |
| chrom | Bio.Data.Bed.Types, Bio.Data.Bed |
| chromEnd | Bio.Data.Bed.Types, Bio.Data.Bed |
| chromStart | Bio.Data.Bed.Types, Bio.Data.Bed |
| clear | Bio.Utils.BitVector |
| closeGenome | Bio.Seq.IO |
| CombineFn | Bio.Motif.Alignment |
| compareBed | Bio.Data.Bed |
| convert | Bio.Data.Bed.Types, Bio.Data.Bed |
| countTagsBinBed | Bio.Data.Bed.Utils |
| countTagsBinBed' | Bio.Data.Bed.Utils |
| coverage | Bio.Utils.Overlap |
| cubPenal | Bio.Motif.Alignment |
| CutoffMotif | |
| 1 (Type/Class) | Bio.Data.Bed.Utils |
| 2 (Data Constructor) | Bio.Data.Bed.Utils |
| cutTreeBy | Bio.Motif.Merge |
| dilute | Bio.Motif.Merge |
| DNA | Bio.Seq |
| downloadData | Bio.RealWorld.GDC |
| EncodeAcc | |
| 1 (Type/Class) | Bio.RealWorld.ID |
| 2 (Data Constructor) | Bio.RealWorld.ID |
| enrichment | Bio.GO |
| EnsemblID | |
| 1 (Type/Class) | Bio.RealWorld.ID |
| 2 (Data Constructor) | Bio.RealWorld.ID |
| expPenal | Bio.Motif.Alignment |
| Ext | Bio.Seq |
| FastaLike | Bio.Data.Fasta |
| fastaReader | Bio.Data.Fasta |
| Fastq | |
| 1 (Type/Class) | Bio.Data.Fastq |
| 2 (Data Constructor) | Bio.Data.Fastq |
| fastqSeq | Bio.Data.Fastq |
| fastqSeqId | Bio.Data.Fastq |
| fastqSeqQual | Bio.Data.Fastq |
| fastqToByteString | Bio.Data.Fastq |
| fetchByGeneNames | Bio.RealWorld.BioGRID |
| fetchSeq | Bio.Data.Bed.Utils |
| fetchSeq' | Bio.Data.Bed.Utils |
| filterFDR | Bio.Utils.Functions |
| findTFBS | Bio.Motif.Search |
| findTFBSSlow | Bio.Motif.Search |
| findTFBSWith | Bio.Motif.Search |
| fragLength | Bio.ChIPSeq.FragLen |
| fromBS | Bio.Seq |
| fromFastaRecord | Bio.Data.Fasta |
| fromID | Bio.RealWorld.ID |
| fromLine | Bio.Data.Bed.Types, Bio.Data.Bed |
| fromMEME | Bio.Motif |
| fromSorted | |
| 1 (Function) | Bio.Data.Bed.Types |
| 2 (Function) | Bio.Utils.Types |
| GAF | |
| 1 (Type/Class) | Bio.GO.Parser |
| 2 (Data Constructor) | Bio.GO.Parser |
| gafAnnotationExtension | Bio.GO.Parser |
| gafAspect | Bio.GO.Parser |
| gafAssignedBy | Bio.GO.Parser |
| gafDate | Bio.GO.Parser |
| gafDb | Bio.GO.Parser |
| gafDbId | Bio.GO.Parser |
| gafDbRef | Bio.GO.Parser |
| gafEvidenceCode | Bio.GO.Parser |
| gafGeneProductID | Bio.GO.Parser |
| gafGoId | Bio.GO.Parser |
| gafName | Bio.GO.Parser |
| gafQualifier | Bio.GO.Parser |
| gafSymbol | Bio.GO.Parser |
| gafSynonym | Bio.GO.Parser |
| gafTaxon | Bio.GO.Parser |
| gafType | Bio.GO.Parser |
| gafWithOrFrom | Bio.GO.Parser |
| gcContent | Bio.Seq |
| gcContentPWM | Bio.Motif |
| Gene | |
| 1 (Type/Class) | Bio.RealWorld.GENCODE |
| 2 (Data Constructor) | Bio.RealWorld.GENCODE |
| geneChrom | Bio.RealWorld.GENCODE |
| geneExon | Bio.RealWorld.GENCODE |
| geneId | Bio.RealWorld.GENCODE |
| geneLeft | Bio.RealWorld.GENCODE |
| geneName | Bio.RealWorld.GENCODE |
| geneRight | Bio.RealWorld.GENCODE |
| geneStrand | Bio.RealWorld.GENCODE |
| geneTranscripts | Bio.RealWorld.GENCODE |
| Genome | Bio.Seq.IO |
| getBamHeader | Bio.Data.Bam |
| getChrom | Bio.Seq.IO |
| getChrSizes | Bio.Seq.IO |
| getFile | Bio.RealWorld.ENCODE |
| getJunction | Bio.RealWorld.UCSC |
| getParentById | Bio.GO |
| getPathways | Bio.RealWorld.Reactome |
| getSeq | Bio.Seq.IO |
| getTSS | Bio.RealWorld.UCSC |
| GO | |
| 1 (Type/Class) | Bio.GO |
| 2 (Data Constructor) | Bio.GO |
| GOID | |
| 1 (Type/Class) | Bio.RealWorld.ID |
| 2 (Data Constructor) | Bio.RealWorld.ID |
| GOId | Bio.GO |
| GOMap | Bio.GO |
| hyperquick | Bio.Utils.Functions |
| ic | Bio.Motif |
| ihs | Bio.Utils.Functions |
| ihs' | Bio.Utils.Functions |
| intersectBed | Bio.Data.Bed |
| intersectBedWith | Bio.Data.Bed |
| intersecting | Bio.Data.Bed |
| intersectSortedBed | Bio.Data.Bed |
| intersectSortedBedWith | Bio.Data.Bed |
| isIntersected | Bio.Data.Bed |
| isOverlapped | Bio.Data.Bed |
| iterativeMerge | Bio.Motif.Merge |
| IUPAC | Bio.Seq |
| jsd | Bio.Utils.Functions |
| jsonFromUrl | Bio.RealWorld.ENCODE |
| KeyWords | |
| 1 (Type/Class) | Bio.RealWorld.ENCODE |
| 2 (Data Constructor) | Bio.RealWorld.ENCODE |
| kld | Bio.Utils.Functions |
| l1 | Bio.Motif.Alignment |
| l2 | Bio.Motif.Alignment |
| l3 | Bio.Motif.Alignment |
| length | Bio.Seq |
| lInf | Bio.Motif.Alignment |
| linPenal | Bio.Motif.Alignment |
| lookup | Bio.RealWorld.Ensembl |
| mapID | Bio.RealWorld.Uniprot |
| maxMatchSc | Bio.Motif.Search |
| mergeBed | Bio.Data.Bed |
| mergeBedWith | Bio.Data.Bed |
| mergePWM | Bio.Motif.Merge |
| mergePWMWeighted | Bio.Motif.Merge |
| mergeSortedBed | Bio.Data.Bed |
| mergeSortedBedWith | Bio.Data.Bed |
| mergeTree | Bio.Motif.Merge |
| mergeTreeWeighted | Bio.Motif.Merge |
| mkCutoffMotif | Bio.Data.Bed.Utils |
| mkIndex | Bio.Seq.IO |
| monoColonalize | Bio.Data.Bed.Utils |
| Motif | |
| 1 (Type/Class) | Bio.Motif |
| 2 (Data Constructor) | Bio.Motif |
| naiveCCWithSmooth | Bio.ChIPSeq.FragLen |
| name | Bio.Data.Bed.Types, Bio.Data.Bed |
| NarrowPeak | |
| 1 (Type/Class) | Bio.Data.Bed.Types, Bio.Data.Bed |
| 2 (Data Constructor) | Bio.Data.Bed.Types |
| npPeak | Bio.Data.Bed.Types, Bio.Data.Bed |
| npPvalue | Bio.Data.Bed.Types, Bio.Data.Bed |
| npQvalue | Bio.Data.Bed.Types, Bio.Data.Bed |
| npSignal | Bio.Data.Bed.Types, Bio.Data.Bed |
| nucleotideFreq | Bio.Seq |
| openGenome | Bio.Seq.IO |
| openUrl | Bio.RealWorld.ENCODE |
| optimalScore | Bio.Motif |
| optimalScoresSuffix | Bio.Motif.Search |
| ordering | Bio.Utils.Types |
| organismIs | Bio.RealWorld.ENCODE |
| overlapFragment | Bio.Utils.Overlap |
| overlapNucl | Bio.Utils.Overlap |
| parseFastqC | Bio.Data.Fastq |
| peakCluster | Bio.Data.Bed.Utils |
| Peptide | Bio.Seq |
| pValueToScore | Bio.Motif |
| pValueToScoreExact | Bio.Motif |
| PWM | |
| 1 (Type/Class) | Bio.Motif |
| 2 (Data Constructor) | Bio.Motif |
| quadPenal | Bio.Motif.Alignment |
| qualitySummary | Bio.Data.Fastq |
| quantileNormalization | Bio.Utils.Functions |
| queryBaseMap | Bio.Data.Bed.Utils |
| queryById | Bio.RealWorld.ENCODE |
| rc | Bio.Seq |
| rcPWM | Bio.Motif |
| readBed | Bio.Data.Bed |
| readDouble | Bio.Utils.Misc |
| readFasta | Bio.Data.Fasta |
| readFasta' | Bio.Data.Fasta |
| readGAF | Bio.GO.Parser |
| readGenes | Bio.RealWorld.GENCODE |
| readInt | Bio.Utils.Misc |
| readMEME | Bio.Motif |
| readOWL | Bio.GO.Parser |
| readOWLAsMap | Bio.GO.Parser |
| readUCSCGenes | Bio.RealWorld.UCSC |
| readUCSCGenes' | Bio.RealWorld.UCSC |
| RNA | Bio.Seq |
| rpkmBed | Bio.Data.Bed.Utils |
| rpkmSortedBed | Bio.Data.Bed.Utils |
| scale | Bio.Utils.Functions |
| scanMotif | Bio.Data.Bed.Utils |
| score | |
| 1 (Function) | Bio.Motif |
| 2 (Function) | Bio.Data.Bed.Types, Bio.Data.Bed |
| scoreCDF | Bio.Motif |
| scores | Bio.Motif |
| scores' | Bio.Motif |
| search | Bio.RealWorld.ENCODE |
| set | Bio.Utils.BitVector |
| showResult | Bio.RealWorld.ENCODE |
| sinkBam | Bio.Data.Bam |
| sinkFastq | Bio.Data.Fastq |
| sinkFastqGzip | Bio.Data.Fastq |
| sinkFileBed | Bio.Data.Bed |
| sinkFileBedGzip | Bio.Data.Bed |
| sinkHandleBed | Bio.Data.Bed |
| size | |
| 1 (Function) | Bio.Utils.BitVector |
| 2 (Function) | Bio.Motif |
| 3 (Function) | Bio.Data.Bed.Types, Bio.Data.Bed |
| sizeOverlapped | Bio.Data.Bed |
| slice | Bio.Seq |
| slideAverage | Bio.Utils.Functions |
| sortBed | Bio.Data.Bed |
| Sorted | |
| 1 (Type/Class) | Bio.Data.Bed.Types |
| 2 (Data Constructor) | Bio.Data.Bed.Types |
| 3 (Type/Class) | Bio.Utils.Types |
| sortedBamToBedPE | Bio.Data.Bam |
| sortedBedToTree | Bio.Data.Bed |
| splitBed | Bio.Data.Bed |
| splitBedBySize | Bio.Data.Bed |
| splitBedBySizeLeft | Bio.Data.Bed |
| splitBedBySizeOverlap | Bio.Data.Bed |
| splitOverlapped | Bio.Data.Bed |
| strand | Bio.Data.Bed.Types, Bio.Data.Bed |
| streamBam | Bio.Data.Bam |
| streamBed | Bio.Data.Bed |
| streamBedGzip | Bio.Data.Bed |
| streamElements | Bio.RealWorld.GENCODE |
| streamFastq | Bio.Data.Fastq |
| streamFastqGzip | Bio.Data.Fastq |
| subPWM | Bio.Motif |
| TAB2 | |
| 1 (Type/Class) | Bio.RealWorld.BioGRID |
| 2 (Data Constructor) | Bio.RealWorld.BioGRID |
| tagCountDistr | Bio.Data.Bed.Utils |
| terms | Bio.RealWorld.ENCODE |
| toBS | Bio.Seq |
| toID | Bio.RealWorld.ID |
| toIUPAC | Bio.Motif |
| toLine | Bio.Data.Bed.Types, Bio.Data.Bed |
| toList | Bio.Utils.BitVector |
| toMEME | Bio.Motif |
| toPWM | Bio.Motif |
| toSorted | Bio.Utils.Types |
| trim | Bio.Motif.Merge |
| trimPolyA | Bio.Data.Fastq |
| truncateCDF | Bio.Motif |
| UCSCGene | |
| 1 (Type/Class) | Bio.RealWorld.UCSC |
| 2 (Data Constructor) | Bio.RealWorld.UCSC |
| UCSCID | |
| 1 (Type/Class) | Bio.RealWorld.ID |
| 2 (Data Constructor) | Bio.RealWorld.ID |
| UniprotID | |
| 1 (Type/Class) | Bio.RealWorld.ID |
| 2 (Data Constructor) | Bio.RealWorld.ID |
| unsafeFreeze | Bio.Utils.BitVector |
| unsafeFromBS | Bio.Seq |
| unsafeToSorted | Bio.Utils.Types |
| withGenome | Bio.Seq.IO |
| writeBed | Bio.Data.Bed |
| writeFasta | Bio.Motif |
| writeMEME | Bio.Motif |
| zeros | Bio.Utils.BitVector |
| _alignId | Bio.RealWorld.UCSC |
| _background | Bio.Data.Bed.Utils |
| _bed | Bio.Data.Bed.Types, Bio.Data.Bed |
| _bed3_chrom | Bio.Data.Bed.Types |
| _bed3_chrom_end | Bio.Data.Bed.Types |
| _bed3_chrom_start | Bio.Data.Bed.Types |
| _bed_chrom | Bio.Data.Bed.Types |
| _bed_chromEnd | Bio.Data.Bed.Types |
| _bed_chromStart | Bio.Data.Bed.Types |
| _bed_name | Bio.Data.Bed.Types |
| _bed_score | Bio.Data.Bed.Types |
| _bed_strand | Bio.Data.Bed.Types |
| _biogridId | Bio.RealWorld.BioGRID |
| _biogridIdA | Bio.RealWorld.BioGRID |
| _biogridIdB | Bio.RealWorld.BioGRID |
| _bpChrom | Bio.Data.Bed.Types |
| _bpEnd | Bio.Data.Bed.Types |
| _bpName | Bio.Data.Bed.Types |
| _bpPvalue | Bio.Data.Bed.Types |
| _bpQvalue | Bio.Data.Bed.Types |
| _bpScore | Bio.Data.Bed.Types |
| _bpSignal | Bio.Data.Bed.Types |
| _bpStart | Bio.Data.Bed.Types |
| _bpStrand | Bio.Data.Bed.Types |
| _cdf | Bio.Data.Bed.Utils |
| _cds | Bio.RealWorld.UCSC |
| _chrom | Bio.RealWorld.UCSC |
| _cutoff | Bio.Data.Bed.Utils |
| _data | Bio.Data.Bed.Types, Bio.Data.Bed |
| _entrezIdA | Bio.RealWorld.BioGRID |
| _entrezIdB | Bio.RealWorld.BioGRID |
| _exons | Bio.RealWorld.UCSC |
| _experimentalSystemName | Bio.RealWorld.BioGRID |
| _experimentalSystemType | Bio.RealWorld.BioGRID |
| _ext_bed | Bio.Data.Bed.Types, Bio.Data.Bed |
| _ext_data | Bio.Data.Bed.Types, Bio.Data.Bed |
| _firstAuthor | Bio.RealWorld.BioGRID |
| _geneName | Bio.RealWorld.UCSC |
| _introns | Bio.RealWorld.UCSC |
| _label | Bio.GO |
| _mat | Bio.Motif |
| _motif_name | Bio.Data.Bed.Utils |
| _motif_pwm | Bio.Data.Bed.Utils |
| _motif_pwm_rc | Bio.Data.Bed.Utils |
| _motif_sigma | Bio.Data.Bed.Utils |
| _motif_sigma_rc | Bio.Data.Bed.Utils |
| _name | Bio.Motif |
| _npChrom | Bio.Data.Bed.Types |
| _npEnd | Bio.Data.Bed.Types |
| _npName | Bio.Data.Bed.Types |
| _npPeak | Bio.Data.Bed.Types |
| _npPvalue | Bio.Data.Bed.Types |
| _npQvalue | Bio.Data.Bed.Types |
| _npScore | Bio.Data.Bed.Types |
| _npSignal | Bio.Data.Bed.Types |
| _npStart | Bio.Data.Bed.Types |
| _npStrand | Bio.Data.Bed.Types |
| _nSites | Bio.Motif |
| _oboId | Bio.GO |
| _oboNS | Bio.GO |
| _organismIdA | Bio.RealWorld.BioGRID |
| _organismIdB | Bio.RealWorld.BioGRID |
| _phenotypes | Bio.RealWorld.BioGRID |
| _proteinId | Bio.RealWorld.UCSC |
| _ptm | Bio.RealWorld.BioGRID |
| _pubmedId | Bio.RealWorld.BioGRID |
| _pwm | Bio.Motif |
| _qualifications | Bio.RealWorld.BioGRID |
| _score | Bio.RealWorld.BioGRID |
| _source | Bio.RealWorld.BioGRID |
| _strand | Bio.RealWorld.UCSC |
| _subProcessOf | Bio.GO |
| _symbolA | Bio.RealWorld.BioGRID |
| _symbolB | Bio.RealWorld.BioGRID |
| _synonymsA | Bio.RealWorld.BioGRID |
| _synonymsB | Bio.RealWorld.BioGRID |
| _systematicNameA | Bio.RealWorld.BioGRID |
| _systematicNameB | Bio.RealWorld.BioGRID |
| _tags | Bio.RealWorld.BioGRID |
| _throughput | Bio.RealWorld.BioGRID |
| _transcript | Bio.RealWorld.UCSC |
| |! | Bio.RealWorld.ENCODE |
| |@ | Bio.RealWorld.ENCODE |